library(tidyverse)
library(Seurat)
library(RColorBrewer)
library(future)
#for 200gb ram
options(future.globals.maxSize = 200000 * 1024^2)
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.5 ✔ purrr 0.3.4 ✔ tibble 3.1.6 ✔ dplyr 1.0.7 ✔ tidyr 1.1.4 ✔ stringr 1.4.0 ✔ readr 1.4.0 ✔ forcats 0.5.1 ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag()
library(ggplot2)
## Load BR_time_course downloaded from GEO:GSE212230
rc.integrated <- readRDS("../../../kallisto-bus/output/Integration/BR_time_course.rds")
# BRZ
brz <- subset(rc.integrated, cells=c('CAACAACTCGCCGAAC_6','AAAGGTATCTCACTCG_1',colnames(rc.integrated)[which((rc.integrated$orig.ident=="sc_43")|(rc.integrated$orig.ident=="sc_50"))]))
table(brz$orig.ident)
sc_12 sc_43 sc_44 sc_50
1 8874 1 5087
Idents(brz) <- "time.celltype.anno.Li.crude"
DefaultAssay(brz) <- "integrated"
brz@assays$integrated@scale.data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
brz@assays$integrated@data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
brz@assays$integrated@scale.data[,'AAAGGTATCTCACTCG_1'] <- rep(0,17732)
brz@assays$integrated@data[,'AAAGGTATCTCACTCG_1'] <- rep(0,17732)
# BL 2 hours
bl2 <- subset(rc.integrated, cells=c('CAACAACTCGCCGAAC_6',colnames(rc.integrated)[which((rc.integrated$orig.ident=="sc_46")|(rc.integrated$orig.ident=="sc_49"))]))
table(bl2$orig.ident)
sc_44 sc_46 sc_49
1 6847 5638
Idents(bl2) <- "time.celltype.anno.Li.crude"
DefaultAssay(bl2) <- "integrated"
bl2
An object of class Seurat 71231 features across 12486 samples within 3 assays Active assay: integrated (17732 features, 17732 variable features) 2 other assays present: RNA, SCT 4 dimensional reductions calculated: pca, umap, umap_3D, umap_2D
bl2@assays$integrated@scale.data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
bl2@assays$integrated@data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
## Load libraries
library(cowplot)
library(ComplexHeatmap)
library(circlize)
library(GeneOverlap)
library(gprofiler2)
library(ggrepel)
library(ggplot2)
Loading required package: grid ======================================== ComplexHeatmap version 2.6.2 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite: Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== ======================================== circlize version 0.4.12 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: https://jokergoo.github.io/circlize_book/book/ If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. This message can be suppressed by: suppressPackageStartupMessages(library(circlize)) ========================================
## Load root atlas downloed from GEO:GSE152766
rc.integrated <- readRDS("../../../kallisto-bus/output/Integration/./Root_Atlas_seu4.rds")
## Downloaded from https://github.com/ohlerlab/COPILOT/tree/master/supp_data
(used.markers <- read_csv("../Validated_Markers.csv"))
── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── cols( Locus = col_character(), Gene = col_character(), Celltype = col_character(), Source = col_character() )
| Locus | Gene | Celltype | Source |
|---|---|---|---|
| <chr> | <chr> | <chr> | <chr> |
| AT1G79840 | GL2 | Atrichoblast | Lee et al., PNAS, 2006 |
| AT3G28540 | AT3G28540 | Columella (1-3th Outer Layer) | Wendrich et al., Science, 2020 |
| AT5G48130 | AT5G48130 | Columella (1-4th Outer Layer) + LRC (3 Vertical Layers from Columella) | Wendrich et al., Science, 2020 |
| AT1G17400 | AT1G17400 | Columella (1-5th Outer Layer) | Wendrich et al., Science, 2020 |
| AT1G33280 | BRN1 | Columella (1st Outer Layer) + LRC (1st +2nd Outer Layer) | Kamiya et al., Development, 2016 |
| AT4G10350 | BRN2 | Columella (1st Outer Layer) + LRC (1st Outer Layer) | Kamiya et al., Development, 2016 |
| AT1G79580 | SMB | Columella + LRC | Kamiya et al., Development, 2016 |
| AT1G62500 | CO2 | Cortex | Heidstra et al., GenesDev, 2004 |
| AT1G62510 | AT1G62510 | Cortex | Denyer et al., Dev Cell, 2019 |
| AT2G40260 | AT2G40260 | Cortex | Wendrich et al., Science, 2020 |
| AT2G29330 | TRI | Cortex + Endodermis | Wendrich et al., Science, 2020 |
| AT3G56220 | AT3G56220 | Cortex + Endodermis | Wendrich et al., Science, 2020 |
| AT3G61930 | AT3G61930 | Distal Columella | SEMITONES |
| AT1G16390 | AT1G16390 | Endodermis | Wendrich et al., Science, 2020 |
| AT1G30750 | AT1G30750 | Endodermis | Wendrich et al., Science, 2020 |
| AT3G54220 | SCR | Endodermis | Birnbaum et al., Science, 2003 |
| AT4G16270 | PER40 | Endodermis | Wendrich et al., Science, 2020 |
| AT5G46600 | ALMT13 | Endodermis | Wendrich et al., Science, 2020 |
| AT5G57620 | MYB36 | Endodermis | Kamiya et al., PNAS, 2015 |
| AT5G14750 | WER | LRC + Atrichoblast | Birnbaum et al., Science, 2003 |
| AT5G19530 | ACL5 | Metaxylem | Wendrich et al., Science, 2020 |
| AT2G31310 | LBD14 | Pericycle Initials | Wendrich et al., Science, 2020 |
| AT1G79430 | APL | Phloem | Bonke et al., Nature,2003 |
| AT4G36410 | UBC17 | Phloem | Wendrich et al., Science, 2020 |
| AT5G04080 | AT5G04080 | Phloem | Wendrich et al., Science, 2020 |
| AT2G22850 | bZIP6 | Phloem;Phloem Pole Pericycle | Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019 |
| AT1G04240 | SHY2 | Procambium + Xylem | Wendrich et al., Science, 2020 |
| AT1G71050 | HIPP20 | Procambium + Xylem | Wendrich et al., Science, 2020 |
| AT1G71930 | VND7 | Protoxylem | Wendrich et al., Science, 2020 |
| AT3G25710 | TMO5 | Protoxylem | Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019 |
| AT4G18780 | CESA8 | Protoxylem | Wendrich et al., Science, 2020 |
| AT2G04025 | RGF3 | Proximal Columella | SEMITONES |
| AT2G18380 | GATA20 | PSE | Frank Qasim Machin et al., The Plant Journal, 2019 |
| AT5G62940 | PEAR1/DOF2.4 | PSE | Miyashima et al., Nature, 2019 |
| AT3G20880 | AT3G20880 | Quiescent Center | Lee et al., PNAS, 2006 |
| AT3G26120 | TEL1 | Quiescent Center | Denyer et al., Dev Cell, 2019 |
| AT5G60810 | RGF1 | Quiescent Center | Matsusaki et al., Science, 2010 |
| AT3G55550 | LECRKS4 | Quiescent Center + Columella | Wendrich et al., Science, 2020 |
| AT3G60650 | AT3G60650 | Quiescent Center + Columella | Wendrich et al., Science, 2020 |
| AT1G66470 | RHD6 | Trichoblast | Menand et al., Science, 2007 |
| AT4G13390 | EXT12 | Trichoblast | Denyer et al., Dev Cell, 2019 |
| AT5G37800 | RSL1 | Trichoblast | Menand et al., Science, 2007 |
| AT5G49270 | COBL9 | Trichoblast | Huang et al., Plant Physiol, 2017 |
| AT5G58010 | LRL3 | Trichoblast | Lee et al., PNAS, 2006 |
| AT2G36120 | DOT1 | Xylem Pole Pericycle | Wendrich et al., Science, 2020 |
| AT4G30450 | XPP | Xylem Pole Pericycle | Wendrich et al., Science, 2020 |
used.markers <- used.markers[-c(3,5,6,7,9,11,12,20,26,27,28,38,39),]
used.markers
| Locus | Gene | Celltype | Source |
|---|---|---|---|
| <chr> | <chr> | <chr> | <chr> |
| AT1G79840 | GL2 | Atrichoblast | Lee et al., PNAS, 2006 |
| AT3G28540 | AT3G28540 | Columella (1-3th Outer Layer) | Wendrich et al., Science, 2020 |
| AT1G17400 | AT1G17400 | Columella (1-5th Outer Layer) | Wendrich et al., Science, 2020 |
| AT1G62500 | CO2 | Cortex | Heidstra et al., GenesDev, 2004 |
| AT2G40260 | AT2G40260 | Cortex | Wendrich et al., Science, 2020 |
| AT3G61930 | AT3G61930 | Distal Columella | SEMITONES |
| AT1G16390 | AT1G16390 | Endodermis | Wendrich et al., Science, 2020 |
| AT1G30750 | AT1G30750 | Endodermis | Wendrich et al., Science, 2020 |
| AT3G54220 | SCR | Endodermis | Birnbaum et al., Science, 2003 |
| AT4G16270 | PER40 | Endodermis | Wendrich et al., Science, 2020 |
| AT5G46600 | ALMT13 | Endodermis | Wendrich et al., Science, 2020 |
| AT5G57620 | MYB36 | Endodermis | Kamiya et al., PNAS, 2015 |
| AT5G19530 | ACL5 | Metaxylem | Wendrich et al., Science, 2020 |
| AT2G31310 | LBD14 | Pericycle Initials | Wendrich et al., Science, 2020 |
| AT1G79430 | APL | Phloem | Bonke et al., Nature,2003 |
| AT4G36410 | UBC17 | Phloem | Wendrich et al., Science, 2020 |
| AT5G04080 | AT5G04080 | Phloem | Wendrich et al., Science, 2020 |
| AT1G71930 | VND7 | Protoxylem | Wendrich et al., Science, 2020 |
| AT3G25710 | TMO5 | Protoxylem | Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019 |
| AT4G18780 | CESA8 | Protoxylem | Wendrich et al., Science, 2020 |
| AT2G04025 | RGF3 | Proximal Columella | SEMITONES |
| AT2G18380 | GATA20 | PSE | Frank Qasim Machin et al., The Plant Journal, 2019 |
| AT5G62940 | PEAR1/DOF2.4 | PSE | Miyashima et al., Nature, 2019 |
| AT3G20880 | AT3G20880 | Quiescent Center | Lee et al., PNAS, 2006 |
| AT3G26120 | TEL1 | Quiescent Center | Denyer et al., Dev Cell, 2019 |
| AT5G60810 | RGF1 | Quiescent Center | Matsusaki et al., Science, 2010 |
| AT1G66470 | RHD6 | Trichoblast | Menand et al., Science, 2007 |
| AT4G13390 | EXT12 | Trichoblast | Denyer et al., Dev Cell, 2019 |
| AT5G37800 | RSL1 | Trichoblast | Menand et al., Science, 2007 |
| AT5G49270 | COBL9 | Trichoblast | Huang et al., Plant Physiol, 2017 |
| AT5G58010 | LRL3 | Trichoblast | Lee et al., PNAS, 2006 |
| AT2G36120 | DOT1 | Xylem Pole Pericycle | Wendrich et al., Science, 2020 |
| AT4G30450 | XPP | Xylem Pole Pericycle | Wendrich et al., Science, 2020 |
used.markers <- rbind(used.markers, c("AT2G36100", "CASP1", "Endodermis", "Trevor"))
used.markers <- rbind(used.markers, c("AT5G64620", "C/VIF2", "Cortex", "Trevor"))
## DE results table from Shahan & Hsu 2022
(Markers_to_plot <- read_csv("../Atlas_time_celltype_Clust_Markers_crude.csv"))
── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── cols( p_val = col_double(), avg_logFC = col_double(), pct.1 = col_double(), pct.2 = col_double(), p_val_adj = col_double(), cluster = col_character(), gene = col_character(), Name = col_character() )
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name |
|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> |
| 0 | 4.359876 | 0.976 | 0.194 | 0 | Transition Domain_Atrichoblast | AT5G01330 | PDC3 |
| 0 | 4.304782 | 0.960 | 0.078 | 0 | Transition Domain_Atrichoblast | AT1G53130 | GRI |
| 0 | 4.077279 | 0.981 | 0.328 | 0 | Transition Domain_Atrichoblast | AT1G41830 | SKS6 |
| 0 | 3.882929 | 0.961 | 0.175 | 0 | Transition Domain_Atrichoblast | AT5G63800 | BGAL6 |
| 0 | 3.805117 | 0.954 | 0.229 | 0 | Transition Domain_Atrichoblast | AT3G63470 | SCPL40 |
| 0 | 3.644233 | 0.981 | 0.125 | 0 | Transition Domain_Atrichoblast | AT1G05660 | AT1G05660 |
| 0 | 3.533744 | 0.787 | 0.087 | 0 | Transition Domain_Atrichoblast | AT5G51490 | PME59 |
| 0 | 3.496127 | 0.967 | 0.323 | 0 | Transition Domain_Atrichoblast | AT1G50430 | DWF5 |
| 0 | 3.421440 | 0.963 | 0.142 | 0 | Transition Domain_Atrichoblast | AT5G44585 | AT5G44585 |
| 0 | 3.411451 | 0.944 | 0.290 | 0 | Transition Domain_Atrichoblast | AT4G27860 | AT4G27860 |
| 0 | 3.385488 | 0.879 | 0.191 | 0 | Transition Domain_Atrichoblast | AT1G18193 | AT1G18193 |
| 0 | 3.339328 | 0.970 | 0.176 | 0 | Transition Domain_Atrichoblast | AT5G02580 | AT5G02580 |
| 0 | 3.333372 | 0.972 | 0.207 | 0 | Transition Domain_Atrichoblast | AT5G15150 | HAT7 |
| 0 | 3.305741 | 0.982 | 0.260 | 0 | Transition Domain_Atrichoblast | AT3G08030 | AT3G08030 |
| 0 | 3.298523 | 0.968 | 0.161 | 0 | Transition Domain_Atrichoblast | AT2G41810 | AT2G41810 |
| 0 | 3.281937 | 0.974 | 0.181 | 0 | Transition Domain_Atrichoblast | AT1G70560 | TAA1 |
| 0 | 3.268023 | 0.901 | 0.179 | 0 | Transition Domain_Atrichoblast | AT4G25250 | PMEI4 |
| 0 | 3.236872 | 0.942 | 0.285 | 0 | Transition Domain_Atrichoblast | AT4G03190 | GRH1 |
| 0 | 3.232729 | 0.960 | 0.163 | 0 | Transition Domain_Atrichoblast | AT4G15230 | ABCG30 |
| 0 | 3.170926 | 0.976 | 0.279 | 0 | Transition Domain_Atrichoblast | AT4G22010 | sks4 |
| 0 | 3.113909 | 0.946 | 0.189 | 0 | Transition Domain_Atrichoblast | AT5G40330 | MYB23 |
| 0 | 3.109084 | 0.925 | 0.107 | 0 | Transition Domain_Atrichoblast | AT2G37260 | WRKY44 |
| 0 | 3.063806 | 0.809 | 0.151 | 0 | Transition Domain_Atrichoblast | AT3G62280 | AT3G62280 |
| 0 | 3.058033 | 0.824 | 0.163 | 0 | Transition Domain_Atrichoblast | AT1G73160 | AT1G73160 |
| 0 | 3.049632 | 0.870 | 0.147 | 0 | Transition Domain_Atrichoblast | AT5G51500 | PME60 |
| 0 | 3.034211 | 0.828 | 0.268 | 0 | Transition Domain_Atrichoblast | AT3G52500 | AT3G52500 |
| 0 | 3.020852 | 0.912 | 0.253 | 0 | Transition Domain_Atrichoblast | AT5G65640 | BHLH93 |
| 0 | 3.007434 | 0.949 | 0.135 | 0 | Transition Domain_Atrichoblast | AT1G54890 | AT1G54890 |
| 0 | 3.006829 | 0.903 | 0.145 | 0 | Transition Domain_Atrichoblast | AT2G04090 | DTX5 |
| 0 | 3.001145 | 0.932 | 0.234 | 0 | Transition Domain_Atrichoblast | AT1G69780 | ATHB-13 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 0.005113615 | 1.3694518 | 0.147 | 0.241 | 1 | Transition Domain_Procambium | AT5G17690 | TFL2 |
| 0.005407906 | 1.5594735 | 0.233 | 0.259 | 1 | Transition Domain_Procambium | AT2G41060 | UBA2B |
| 0.005469202 | 1.4256391 | 0.221 | 0.133 | 1 | Transition Domain_Procambium | AT2G17590 | AT2G17590 |
| 0.005772335 | 0.7654884 | 0.319 | 0.235 | 1 | Transition Domain_Procambium | AT5G56890 | AT5G56890 |
| 0.005784713 | 0.8848589 | 0.442 | 0.299 | 1 | Transition Domain_Procambium | AT5G54440 | TRS130 |
| 0.005808582 | 1.8340622 | 0.454 | 0.159 | 1 | Transition Domain_Procambium | AT4G09105 | AT4G09105 |
| 0.006015583 | 1.4758978 | 0.325 | 0.143 | 1 | Transition Domain_Procambium | AT2G23970 | GGP5 |
| 0.006147177 | 0.4576765 | 0.472 | 0.223 | 1 | Transition Domain_Procambium | AT4G36530 | AT4G36530 |
| 0.006345547 | 1.2288016 | 0.387 | 0.175 | 1 | Transition Domain_Procambium | AT4G18375 | AT4G18375 |
| 0.006457260 | 0.9352226 | 0.319 | 0.218 | 1 | Transition Domain_Procambium | AT1G58150 | AT1G58150 |
| 0.006540872 | 1.5822467 | 0.245 | 0.232 | 1 | Transition Domain_Procambium | AT4G04190 | AT4G04190 |
| 0.006547528 | 0.5522590 | 0.448 | 0.272 | 1 | Transition Domain_Procambium | AT2G27210 | BSL3 |
| 0.006697961 | 0.7703493 | 0.399 | 0.164 | 1 | Transition Domain_Procambium | AT1G63240 | AT1G63240 |
| 0.007048779 | 1.1145574 | 0.135 | 0.131 | 1 | Transition Domain_Procambium | AT2G22540 | SVP |
| 0.007269855 | 1.5258477 | 0.387 | 0.063 | 1 | Transition Domain_Procambium | AT2G25060 | ENODL14 |
| 0.007315341 | 0.7692672 | 0.454 | 0.147 | 1 | Transition Domain_Procambium | AT2G20850 | SRF1 |
| 0.007525159 | 1.4744451 | 0.258 | 0.139 | 1 | Transition Domain_Procambium | AT2G09445 | AT2G09445 |
| 0.007549643 | 1.5455848 | 0.270 | 0.210 | 1 | Transition Domain_Procambium | AT4G09490 | AT4G09490 |
| 0.007586351 | 1.2293376 | 0.331 | 0.194 | 1 | Transition Domain_Procambium | AT3G23330 | PCMP-H32 |
| 0.007632690 | 2.5350602 | 0.356 | 0.295 | 1 | Transition Domain_Procambium | AT3G04680 | CLPS3 |
| 0.007644926 | 0.9538205 | 0.282 | 0.138 | 1 | Transition Domain_Procambium | AT3G16250 | PNSB3 |
| 0.007939177 | 1.6851117 | 0.294 | 0.239 | 1 | Transition Domain_Procambium | AT3G01600 | anac044 |
| 0.007994449 | 1.3394202 | 0.160 | 0.256 | 1 | Transition Domain_Procambium | AT3G07740 | ADA2A |
| 0.008262217 | 1.8320488 | 0.387 | 0.144 | 1 | Transition Domain_Procambium | AT1G14350 | MYB124 |
| 0.008604453 | 0.8478655 | 0.258 | 0.237 | 1 | Transition Domain_Procambium | AT5G35100 | AT5G35100 |
| 0.009338881 | 0.5846969 | 0.411 | 0.221 | 1 | Transition Domain_Procambium | AT3G48120 | AT3G48120 |
| 0.009371151 | 1.5723879 | 0.387 | 0.273 | 1 | Transition Domain_Procambium | AT1G02750 | DI19-2 |
| 0.009488593 | 1.0210781 | 0.454 | 0.190 | 1 | Transition Domain_Procambium | AT5G65710 | HSL2 |
| 0.009539965 | 0.4416200 | 0.356 | 0.115 | 1 | Transition Domain_Procambium | AT4G20940 | AT4G20940 |
| 0.009594586 | 0.7898078 | 0.190 | 0.236 | 1 | Transition Domain_Procambium | AT2G07776 | AT2G07776 |
Markers_to_plot <- Markers_to_plot %>% mutate(pct.diff = pct.1-pct.2) %>% mutate(pct.diff.rank = rank(pct.diff)) %>% mutate(avg_logFC.rank = rank(avg_logFC)) %>% mutate(combined.rank = pct.diff.rank+avg_logFC.rank) %>% filter(p_val_adj<=0.01)
Markers_to_plot[which(Markers_to_plot$Name=="SCR"),]
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name | pct.diff | pct.diff.rank | avg_logFC.rank | combined.rank |
|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> |
| 0.000000e+00 | 3.5262298 | 0.675 | 0.082 | 0.000000e+00 | Elongation_Endodermis | AT3G54220 | SCR | 0.593 | 116323.5 | 123163 | 239486.5 |
| 6.838647e-107 | 3.8018223 | 0.838 | 0.119 | 1.197652e-102 | Transition Domain_Endodermis | AT3G54220 | SCR | 0.719 | 122780.5 | 123801 | 246581.5 |
| 1.170162e-97 | 0.5555261 | 0.489 | 0.110 | 2.049304e-93 | Maturation_Endodermis | AT3G54220 | SCR | 0.379 | 91558.0 | 33211 | 124769.0 |
| 1.348769e-40 | 2.3336712 | 0.393 | 0.118 | 2.362099e-36 | Proliferation Domain_Endodermis | AT3G54220 | SCR | 0.275 | 72218.5 | 114812 | 187030.5 |
vMarkers_to_plot <- Markers_to_plot[(Markers_to_plot$gene %in% used.markers$Locus),]
Markers_to_plot[which(Markers_to_plot$Name=="CASP1"),]
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name | pct.diff | pct.diff.rank | avg_logFC.rank | combined.rank |
|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> |
| 2.457018e-37 | 1.299689 | 0.279 | 0.107 | 4.302975e-33 | Elongation_Endodermis | AT2G36100 | CASP1 | 0.172 | 50385.0 | 87181 | 137566.0 |
| 0.000000e+00 | 4.205272 | 0.976 | 0.093 | 0.000000e+00 | Maturation_Endodermis | AT2G36100 | CASP1 | 0.883 | 124787.5 | 124388 | 249175.5 |
Markers_to_plot[which(Markers_to_plot$Name=="C/VIF2"),]
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name | pct.diff | pct.diff.rank | avg_logFC.rank | combined.rank |
|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> |
| 0.000000e+00 | 4.2214263 | 0.842 | 0.107 | 0.000000e+00 | Elongation_Cortex | AT5G64620 | C/VIF2 | 0.735 | 123209 | 124402 | 247611 |
| 1.511211e-239 | 0.6067237 | 0.537 | 0.140 | 2.646584e-235 | Maturation_Cortex | AT5G64620 | C/VIF2 | 0.397 | 94449 | 38211 | 132660 |
| 0.000000e+00 | 2.1115062 | 0.841 | 0.135 | 0.000000e+00 | Transition Domain_Cortex | AT5G64620 | C/VIF2 | 0.706 | 122422 | 111376 | 233798 |
vMarkers_to_plot
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name | pct.diff | pct.diff.rank | avg_logFC.rank | combined.rank |
|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> |
| 0.000000e+00 | 2.8800395 | 0.876 | 0.121 | 0.000000e+00 | Transition Domain_Atrichoblast | AT1G79840 | GL2 | 0.755 | 123623.5 | 120054 | 243677.5 |
| 3.895454e-245 | 2.0378491 | 0.587 | 0.116 | 6.822109e-241 | Elongation_Atrichoblast | AT1G79840 | GL2 | 0.471 | 104568.0 | 110077 | 214645.0 |
| 0.000000e+00 | 4.2214263 | 0.842 | 0.107 | 0.000000e+00 | Elongation_Cortex | AT5G64620 | C/VIF2 | 0.735 | 123209.0 | 124402 | 247611.0 |
| 0.000000e+00 | 0.2912310 | 0.268 | 0.071 | 0.000000e+00 | Proximal Lateral Root Cap | AT2G04025 | RGF3 | 0.197 | 55760.5 | 4826 | 60586.5 |
| 1.511211e-239 | 0.6067237 | 0.537 | 0.140 | 2.646584e-235 | Maturation_Cortex | AT5G64620 | C/VIF2 | 0.397 | 94449.0 | 38211 | 132660.0 |
| 0.000000e+00 | 0.2989555 | 0.400 | 0.092 | 0.000000e+00 | Elongation_Pericycle | AT3G25710 | BHLH32 | 0.308 | 78885.5 | 5751 | 84636.5 |
| 3.236570e-26 | 2.6419540 | 0.372 | 0.066 | 5.668206e-22 | Elongation_Pericycle | AT2G31310 | LBD14 | 0.306 | 78378.0 | 118188 | 196566.0 |
| 0.000000e+00 | 3.6497667 | 0.691 | 0.015 | 0.000000e+00 | Elongation_Xylem | AT4G18780 | CESA8 | 0.676 | 121223.5 | 123467 | 244690.5 |
| 0.000000e+00 | 3.5093015 | 0.766 | 0.017 | 0.000000e+00 | Elongation_Xylem | AT1G71930 | NAC030 | 0.749 | 123507.5 | 123107 | 246614.5 |
| 0.000000e+00 | 3.2886888 | 0.829 | 0.100 | 0.000000e+00 | Elongation_Xylem | AT3G25710 | BHLH32 | 0.729 | 123062.0 | 122300 | 245362.0 |
| 1.023165e-12 | 1.6169463 | 0.380 | 0.114 | 1.791870e-08 | Maturation_Pericycle | AT3G25710 | BHLH32 | 0.266 | 70486.0 | 99781 | 170267.0 |
| 0.000000e+00 | 5.8474096 | 0.750 | 0.010 | 0.000000e+00 | Elongation_Endodermis | AT1G16390 | OCT3 | 0.740 | 123318.5 | 124975 | 248293.5 |
| 0.000000e+00 | 5.7307579 | 0.799 | 0.022 | 0.000000e+00 | Elongation_Endodermis | AT4G16270 | PER40 | 0.777 | 123973.5 | 124969 | 248942.5 |
| 0.000000e+00 | 4.7560838 | 0.990 | 0.044 | 0.000000e+00 | Elongation_Endodermis | AT5G57620 | MYB36 | 0.946 | 124949.0 | 124741 | 249690.0 |
| 0.000000e+00 | 4.5832113 | 0.728 | 0.043 | 0.000000e+00 | Elongation_Endodermis | AT5G46600 | ALMT13 | 0.685 | 121612.0 | 124655 | 246267.0 |
| 0.000000e+00 | 3.5262298 | 0.675 | 0.082 | 0.000000e+00 | Elongation_Endodermis | AT3G54220 | SCR | 0.593 | 116323.5 | 123163 | 239486.5 |
| 1.722081e-285 | 0.5823483 | 0.125 | 0.088 | 3.015881e-281 | Elongation_Endodermis | AT1G30750 | AT1G30750 | 0.037 | 23727.5 | 35894 | 59621.5 |
| 2.457018e-37 | 1.2996888 | 0.279 | 0.107 | 4.302975e-33 | Elongation_Endodermis | AT2G36100 | CASP1 | 0.172 | 50385.0 | 87181 | 137566.0 |
| 0.000000e+00 | 4.3325176 | 0.893 | 0.031 | 0.000000e+00 | Elongation_Phloem | AT5G62940 | DOF5.6 | 0.862 | 124694.5 | 124487 | 249181.5 |
| 0.000000e+00 | 4.0380863 | 0.984 | 0.032 | 0.000000e+00 | Elongation_Phloem | AT1G79430 | APL | 0.952 | 124962.5 | 124167 | 249129.5 |
| 0.000000e+00 | 4.0194403 | 0.997 | 0.050 | 0.000000e+00 | Elongation_Phloem | AT5G04080 | AT5G04080 | 0.947 | 124953.5 | 124147 | 249100.5 |
| 0.000000e+00 | 3.9999511 | 0.531 | 0.014 | 0.000000e+00 | Elongation_Phloem | AT2G18380 | GATA20 | 0.517 | 109844.0 | 124121 | 233965.0 |
| 1.034523e-301 | 4.2939897 | 0.671 | 0.034 | 1.811760e-297 | Elongation_Phloem | AT4G36410 | UBC17 | 0.637 | 119127.0 | 124458 | 243585.0 |
| 2.081747e-10 | 0.7236844 | 0.259 | 0.121 | 3.645764e-06 | Maturation_Procambium | AT3G25710 | BHLH32 | 0.138 | 42883.0 | 48935 | 91818.0 |
| 0.000000e+00 | 2.6326692 | 0.879 | 0.114 | 0.000000e+00 | Proliferation Domain_Atrichoblast | AT1G79840 | GL2 | 0.765 | 123805.5 | 118097 | 241902.5 |
| 4.688818e-94 | 0.4693028 | 0.172 | 0.091 | 8.211527e-90 | Proliferation Domain_Atrichoblast | AT2G04025 | RGF3 | 0.081 | 31408.0 | 24444 | 55852.0 |
| 0.000000e+00 | 5.1483876 | 0.768 | 0.026 | 0.000000e+00 | Maturation_Trichoblast | AT4G13390 | AT4G13390 | 0.742 | 123362.5 | 124879 | 248241.5 |
| 0.000000e+00 | 4.9697672 | 0.994 | 0.063 | 0.000000e+00 | Maturation_Trichoblast | AT5G58010 | BHLH82 | 0.931 | 124917.0 | 124818 | 249735.0 |
| 0.000000e+00 | 3.3588530 | 0.818 | 0.093 | 0.000000e+00 | Maturation_Trichoblast | AT1G66470 | BHLH83 | 0.725 | 122945.5 | 122583 | 245528.5 |
| 1.783170e-201 | 2.0249158 | 0.540 | 0.069 | 3.122865e-197 | Maturation_Trichoblast | AT5G49270 | COBL9 | 0.471 | 104622.0 | 109851 | 214473.0 |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| 1.987023e-25 | 1.5746564 | 0.154 | 0.035 | 3.479873e-21 | Proliferation Domain_Cortex | AT1G17400 | AT1G17400 | 0.119 | 38962.5 | 98318 | 137280.5 |
| 2.272772e-259 | 1.3314433 | 0.663 | 0.111 | 3.980305e-255 | Proliferation Domain_Trichoblast | AT1G66470 | BHLH83 | 0.552 | 113036.0 | 88698 | 201734.0 |
| 1.633657e-97 | 2.7366102 | 0.560 | 0.080 | 2.861023e-93 | Proliferation Domain_Trichoblast | AT5G37800 | BHLH86 | 0.480 | 105740.0 | 118956 | 224696.0 |
| 0.000000e+00 | 3.5579629 | 0.979 | 0.051 | 0.000000e+00 | Maturation_Phloem | AT1G79430 | APL | 0.928 | 124906.0 | 123244 | 248150.0 |
| 0.000000e+00 | 3.4282083 | 0.997 | 0.069 | 0.000000e+00 | Maturation_Phloem | AT5G04080 | AT5G04080 | 0.928 | 124906.0 | 122854 | 247760.0 |
| 2.160486e-237 | 3.4280374 | 0.815 | 0.046 | 3.783659e-233 | Maturation_Phloem | AT4G36410 | UBC17 | 0.769 | 123864.0 | 122853 | 246717.0 |
| 3.042751e-197 | 2.7885168 | 0.588 | 0.024 | 5.328771e-193 | Maturation_Phloem | AT2G18380 | GATA20 | 0.564 | 114041.5 | 119378 | 233419.5 |
| 5.223582e-83 | 2.6625315 | 0.513 | 0.050 | 9.148059e-79 | Maturation_Phloem | AT5G62940 | DOF5.6 | 0.463 | 103654.5 | 118384 | 222038.5 |
| 0.000000e+00 | 4.6718810 | 0.878 | 0.068 | 0.000000e+00 | Maturation_Endodermis | AT1G30750 | AT1G30750 | 0.810 | 124354.0 | 124699 | 249053.0 |
| 0.000000e+00 | 4.2052718 | 0.976 | 0.093 | 0.000000e+00 | Maturation_Endodermis | AT2G36100 | CASP1 | 0.883 | 124787.5 | 124388 | 249175.5 |
| 0.000000e+00 | 1.0532810 | 0.783 | 0.085 | 0.000000e+00 | Maturation_Endodermis | AT5G57620 | MYB36 | 0.698 | 122167.5 | 73496 | 195663.5 |
| 0.000000e+00 | 0.2770799 | 0.700 | 0.069 | 0.000000e+00 | Maturation_Endodermis | AT5G46600 | ALMT13 | 0.631 | 118800.0 | 3149 | 121949.0 |
| 1.170162e-97 | 0.5555261 | 0.489 | 0.110 | 2.049304e-93 | Maturation_Endodermis | AT3G54220 | SCR | 0.379 | 91558.0 | 33211 | 124769.0 |
| 1.426204e-200 | 3.4548715 | 1.000 | 0.055 | 2.497711e-196 | Transition Domain_Phloem | AT1G79430 | APL | 0.945 | 124946.0 | 122940 | 247886.0 |
| 8.582098e-196 | 3.1635191 | 0.997 | 0.073 | 1.502983e-191 | Transition Domain_Phloem | AT5G04080 | AT5G04080 | 0.924 | 124899.0 | 121693 | 246592.0 |
| 7.475570e-162 | 2.9611038 | 0.901 | 0.051 | 1.309197e-157 | Transition Domain_Phloem | AT5G62940 | DOF5.6 | 0.850 | 124638.5 | 120562 | 245200.5 |
| 1.000854e-72 | 2.6656720 | 0.704 | 0.049 | 1.752796e-68 | Transition Domain_Phloem | AT4G36410 | UBC17 | 0.655 | 120103.5 | 118413 | 238516.5 |
| 3.784330e-15 | 3.3186870 | 0.484 | 0.026 | 6.627497e-11 | Transition Domain_Phloem | AT2G18380 | GATA20 | 0.458 | 102959.5 | 122429 | 225388.5 |
| 6.287865e-50 | 0.3878038 | 0.534 | 0.085 | 1.101194e-45 | Proliferation Domain_Endodermis | AT5G37800 | BHLH86 | 0.449 | 101888.5 | 15800 | 117688.5 |
| 1.348769e-40 | 2.3336712 | 0.393 | 0.118 | 2.362099e-36 | Proliferation Domain_Endodermis | AT3G54220 | SCR | 0.275 | 72218.5 | 114812 | 187030.5 |
| 1.770651e-37 | 0.9020013 | 0.478 | 0.120 | 3.100942e-33 | Proliferation Domain_Endodermis | AT3G25710 | BHLH32 | 0.358 | 88055.0 | 63272 | 151327.0 |
| 1.084228e-95 | 3.7542288 | 0.987 | 0.092 | 1.898808e-91 | Proliferation Domain_Quiescent Center | AT2G04025 | RGF3 | 0.895 | 124829.0 | 123719 | 248548.0 |
| 1.317794e-49 | 5.0088854 | 0.816 | 0.175 | 2.307853e-45 | Proliferation Domain_Quiescent Center | AT3G26120 | TEL1 | 0.641 | 119330.0 | 124834 | 244164.0 |
| 1.588789e-22 | 4.4788046 | 0.658 | 0.035 | 2.782447e-18 | Proliferation Domain_Quiescent Center | AT1G17400 | AT1G17400 | 0.623 | 118299.5 | 124606 | 242905.5 |
| 2.477925e-54 | 2.0549175 | 0.911 | 0.040 | 4.339591e-50 | Proliferation Domain_Xylem | AT1G71930 | NAC030 | 0.871 | 124741.5 | 110432 | 235173.5 |
| 1.201159e-53 | 3.7425432 | 0.920 | 0.122 | 2.103590e-49 | Proliferation Domain_Xylem | AT3G25710 | BHLH32 | 0.798 | 124225.0 | 123693 | 247918.0 |
| 7.351989e-72 | 3.5364184 | 0.926 | 0.122 | 1.287554e-67 | Transition Domain_Xylem | AT3G25710 | BHLH32 | 0.804 | 124286.5 | 123193 | 247479.5 |
| 9.282368e-59 | 2.6364459 | 0.868 | 0.040 | 1.625621e-54 | Transition Domain_Xylem | AT1G71930 | NAC030 | 0.828 | 124509.0 | 118135 | 242644.0 |
| 1.673278e-18 | 0.3849318 | 0.282 | 0.057 | 2.930411e-14 | Transition Domain_Procambium | AT1G79430 | APL | 0.225 | 61763.0 | 15500 | 77263.0 |
| 8.080235e-10 | 1.1675655 | 0.123 | 0.028 | 1.415092e-05 | Transition Domain_Procambium | AT2G18380 | GATA20 | 0.095 | 34187.0 | 80240 | 114427.0 |
vMarkers_to_plot <- vMarkers_to_plot %>% group_by(gene) %>% top_n(1, combined.rank) %>% group_by(cluster) %>% top_n(1, combined.rank) %>% mutate(source=1)
iMarkers_to_plot <- Markers_to_plot %>% group_by(gene) %>% top_n(1, combined.rank) %>% group_by(cluster) %>% top_n(1, combined.rank) %>% mutate(source=2)
Markers_to_plot <- bind_rows(vMarkers_to_plot,iMarkers_to_plot)
Markers_to_plot <- Markers_to_plot %>% group_by(cluster) %>% top_n(1,-source)
Markers_to_plot <- Markers_to_plot %>% mutate(timezone=gsub("_.*$","",cluster)) %>% mutate(celltype=gsub("^.*_","",cluster))
Markers_to_plot
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene | Name | pct.diff | pct.diff.rank | avg_logFC.rank | combined.rank | source | timezone | celltype |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> |
| 0.000000e+00 | 2.880039 | 0.876 | 0.121 | 0.000000e+00 | Transition Domain_Atrichoblast | AT1G79840 | GL2 | 0.755 | 123623.5 | 120054 | 243677.5 | 1 | Transition Domain | Atrichoblast |
| 0.000000e+00 | 4.221426 | 0.842 | 0.107 | 0.000000e+00 | Elongation_Cortex | AT5G64620 | C/VIF2 | 0.735 | 123209.0 | 124402 | 247611.0 | 1 | Elongation | Cortex |
| 0.000000e+00 | 4.756084 | 0.990 | 0.044 | 0.000000e+00 | Elongation_Endodermis | AT5G57620 | MYB36 | 0.946 | 124949.0 | 124741 | 249690.0 | 1 | Elongation | Endodermis |
| 0.000000e+00 | 4.332518 | 0.893 | 0.031 | 0.000000e+00 | Elongation_Phloem | AT5G62940 | DOF5.6 | 0.862 | 124694.5 | 124487 | 249181.5 | 1 | Elongation | Phloem |
| 0.000000e+00 | 4.969767 | 0.994 | 0.063 | 0.000000e+00 | Maturation_Trichoblast | AT5G58010 | BHLH82 | 0.931 | 124917.0 | 124818 | 249735.0 | 1 | Maturation | Trichoblast |
| 2.947593e-86 | 2.952604 | 0.647 | 0.092 | 5.162120e-82 | Proliferation Domain_Pericycle | AT2G31310 | LBD14 | 0.555 | 113332.5 | 120506 | 233838.5 | 1 | Proliferation Domain | Pericycle |
| 6.838647e-107 | 3.801822 | 0.838 | 0.119 | 1.197652e-102 | Transition Domain_Endodermis | AT3G54220 | SCR | 0.719 | 122780.5 | 123801 | 246581.5 | 1 | Transition Domain | Endodermis |
| 0.000000e+00 | 3.994196 | 0.745 | 0.065 | 0.000000e+00 | Elongation_Trichoblast | AT5G49270 | COBL9 | 0.680 | 121400.0 | 124108 | 245508.0 | 1 | Elongation | Trichoblast |
| 0.000000e+00 | 4.157532 | 0.964 | 0.079 | 0.000000e+00 | Proximal Columella | AT2G04025 | RGF3 | 0.885 | 124794.0 | 124337 | 249131.0 | 1 | Proximal Columella | Proximal Columella |
| 0.000000e+00 | 4.351426 | 0.984 | 0.031 | 0.000000e+00 | Maturation_Xylem | AT1G71930 | NAC030 | 0.953 | 124965.5 | 124507 | 249472.5 | 1 | Maturation | Xylem |
| 1.633657e-97 | 2.736610 | 0.560 | 0.080 | 2.861023e-93 | Proliferation Domain_Trichoblast | AT5G37800 | BHLH86 | 0.480 | 105740.0 | 118956 | 224696.0 | 1 | Proliferation Domain | Trichoblast |
| 2.160486e-237 | 3.428037 | 0.815 | 0.046 | 3.783659e-233 | Maturation_Phloem | AT4G36410 | UBC17 | 0.769 | 123864.0 | 122853 | 246717.0 | 1 | Maturation | Phloem |
| 0.000000e+00 | 4.205272 | 0.976 | 0.093 | 0.000000e+00 | Maturation_Endodermis | AT2G36100 | CASP1 | 0.883 | 124787.5 | 124388 | 249175.5 | 1 | Maturation | Endodermis |
| 1.317794e-49 | 5.008885 | 0.816 | 0.175 | 2.307853e-45 | Proliferation Domain_Quiescent Center | AT3G26120 | TEL1 | 0.641 | 119330.0 | 124834 | 244164.0 | 1 | Proliferation Domain | Quiescent Center |
| 1.201159e-53 | 3.742543 | 0.920 | 0.122 | 2.103590e-49 | Proliferation Domain_Xylem | AT3G25710 | BHLH32 | 0.798 | 124225.0 | 123693 | 247918.0 | 1 | Proliferation Domain | Xylem |
| 0.000000e+00 | 4.986413 | 0.817 | 0.034 | 0.000000e+00 | Elongation_Atrichoblast | AT3G19320 | AT3G19320 | 0.783 | 124043.0 | 124826 | 248869.0 | 2 | Elongation | Atrichoblast |
| 0.000000e+00 | 4.448936 | 0.960 | 0.084 | 0.000000e+00 | Distal Columella | AT1G05010 | ACO4 | 0.876 | 124764.5 | 124589 | 249353.5 | 2 | Distal Columella | Distal Columella |
| 0.000000e+00 | 4.449222 | 0.878 | 0.075 | 0.000000e+00 | Proximal Lateral Root Cap | AT5G60520 | AT5G60520 | 0.803 | 124278.5 | 124590 | 248868.5 | 2 | Proximal Lateral Root Cap | Proximal Lateral Root Cap |
| 0.000000e+00 | 4.124382 | 0.918 | 0.123 | 0.000000e+00 | Maturation_Cortex | AT4G09760 | AT4G09760 | 0.795 | 124201.0 | 124293 | 248494.0 | 2 | Maturation | Cortex |
| 0.000000e+00 | 4.145240 | 0.790 | 0.072 | 0.000000e+00 | Elongation_Pericycle | AT3G45700 | NPF2.4 | 0.718 | 122769.0 | 124316 | 247085.0 | 2 | Elongation | Pericycle |
| 0.000000e+00 | 5.872471 | 0.973 | 0.016 | 0.000000e+00 | Elongation_Xylem | AT1G79620 | AT1G79620 | 0.957 | 124974.5 | 124977 | 249951.5 | 2 | Elongation | Xylem |
| 0.000000e+00 | 4.673547 | 0.957 | 0.081 | 0.000000e+00 | Maturation_Pericycle | AT5G43180 | AT5G43180 | 0.876 | 124764.5 | 124701 | 249465.5 | 2 | Maturation | Pericycle |
| 0.000000e+00 | 3.992237 | 0.915 | 0.097 | 0.000000e+00 | Maturation_Procambium | AT1G61660 | BHLH112 | 0.818 | 124424.0 | 124101 | 248525.0 | 2 | Maturation | Procambium |
| 0.000000e+00 | 5.013528 | 0.962 | 0.055 | 0.000000e+00 | Elongation_Procambium | AT4G14650 | AT4G14650 | 0.907 | 124855.0 | 124836 | 249691.0 | 2 | Elongation | Procambium |
| 0.000000e+00 | 4.244605 | 0.896 | 0.058 | 0.000000e+00 | Proliferation Domain_Atrichoblast | AT1G27950 | LTPG1 | 0.838 | 124567.5 | 124427 | 248994.5 | 2 | Proliferation Domain | Atrichoblast |
| 0.000000e+00 | 3.836213 | 0.955 | 0.134 | 0.000000e+00 | Maturation_Atrichoblast | AT3G01970 | WRKY45 | 0.821 | 124448.5 | 123856 | 248304.5 | 2 | Maturation | Atrichoblast |
| 0.000000e+00 | 4.303436 | 0.883 | 0.128 | 0.000000e+00 | Distal Lateral Root Cap | AT2G42890 | ML2 | 0.755 | 123623.5 | 124462 | 248085.5 | 2 | Distal Lateral Root Cap | Distal Lateral Root Cap |
| 0.000000e+00 | 3.424465 | 0.850 | 0.110 | 0.000000e+00 | Transition Domain_Trichoblast | AT1G27140 | GSTU14 | 0.740 | 123318.5 | 122839 | 246157.5 | 2 | Transition Domain | Trichoblast |
| 0.000000e+00 | 3.830770 | 0.973 | 0.095 | 0.000000e+00 | Transition Domain_Cortex | AT1G12845 | AT1G12845 | 0.878 | 124772.5 | 123849 | 248621.5 | 2 | Transition Domain | Cortex |
| 0.000000e+00 | 2.907688 | 0.855 | 0.114 | 0.000000e+00 | Transition Domain_Pericycle | AT2G26040 | PYL2 | 0.741 | 123339.0 | 120229 | 243568.0 | 2 | Transition Domain | Pericycle |
| 8.601397e-66 | 4.336299 | 0.957 | 0.065 | 1.506363e-61 | Proliferation Domain_Phloem | AT5G62960 | AT5G62960 | 0.892 | 124820.0 | 124493 | 249313.0 | 2 | Proliferation Domain | Phloem |
| 0.000000e+00 | 3.372740 | 0.885 | 0.119 | 0.000000e+00 | Proliferation Domain_Cortex | AT3G15240 | AT3G15240 | 0.766 | 123819.0 | 122643 | 246462.0 | 2 | Proliferation Domain | Cortex |
| 4.208077e-196 | 4.268367 | 0.982 | 0.074 | 7.369606e-192 | Transition Domain_Phloem | AT2G39830 | DAR2 | 0.908 | 124861.0 | 124442 | 249303.0 | 2 | Transition Domain | Phloem |
| 0.000000e+00 | 3.494906 | 0.927 | 0.213 | 0.000000e+00 | Proliferation Domain_Endodermis | AT3G10610 | RPS17C | 0.714 | 122662.5 | 123065 | 245727.5 | 2 | Proliferation Domain | Endodermis |
| 6.191777e-70 | 4.362727 | 0.919 | 0.089 | 1.084366e-65 | Transition Domain_Xylem | AT2G34060 | PER19 | 0.830 | 124523.0 | 124519 | 249042.0 | 2 | Transition Domain | Xylem |
| 7.148410e-27 | 3.877156 | 0.978 | 0.174 | 1.251901e-22 | Proliferation Domain_Procambium | AT3G59680 | AT3G59680 | 0.804 | 124286.5 | 123915 | 248201.5 | 2 | Proliferation Domain | Procambium |
| 7.062549e-79 | 4.503423 | 0.926 | 0.055 | 1.236864e-74 | Transition Domain_Procambium | AT4G22900 | AT4G22900 | 0.871 | 124741.5 | 124623 | 249364.5 | 2 | Transition Domain | Procambium |
order <- c("Proliferation Domain_Quiescent Center","Proximal Columella","Distal Columella", "Proximal Lateral Root Cap", "Distal Lateral Root Cap",
"Proliferation Domain_Atrichoblast","Transition Domain_Atrichoblast","Elongation_Atrichoblast","Maturation_Atrichoblast",
"Proliferation Domain_Trichoblast", "Transition Domain_Trichoblast", "Elongation_Trichoblast", "Maturation_Trichoblast",
"Proliferation Domain_Cortex", "Transition Domain_Cortex", "Elongation_Cortex", "Maturation_Cortex",
"Proliferation Domain_Endodermis","Transition Domain_Endodermis", "Elongation_Endodermis", "Maturation_Endodermis",
"Proliferation Domain_Procambium", "Transition Domain_Procambium", "Elongation_Procambium", "Maturation_Procambium",
"Proliferation Domain_Pericycle", "Transition Domain_Pericycle", "Elongation_Pericycle", "Maturation_Pericycle",
"Proliferation Domain_Phloem", "Transition Domain_Phloem", "Elongation_Phloem", "Maturation_Phloem",
"Proliferation Domain_Xylem", "Transition Domain_Xylem", "Elongation_Xylem", "Maturation_Xylem")
Markers_to_plot <- Markers_to_plot[match(order, Markers_to_plot$cluster),]
(c_levels <- unique(Markers_to_plot$cluster))
ct_to_plt_Names <- rev(Markers_to_plot$Name)
ct_to_plt_genes <- rev(Markers_to_plot$gene)
(labels <- (ct_to_plt_Names))
table(rc.integrated$time.celltype.anno.Li.crude)
Proliferation Domain_Quiescent Center Proximal Columella
91 1282
Distal Columella Proximal Lateral Root Cap
5846 16790
Distal Lateral Root Cap Proliferation Domain_Atrichoblast
4864 3725
Transition Domain_Atrichoblast Elongation_Atrichoblast
2354 3772
Maturation_Atrichoblast Proliferation Domain_Trichoblast
2434 1648
Transition Domain_Trichoblast Elongation_Trichoblast
2514 3492
Maturation_Trichoblast Proliferation Domain_Cortex
3560 696
Transition Domain_Cortex Elongation_Cortex
2121 4123
Maturation_Cortex Proliferation Domain_Endodermis
1124 921
Transition Domain_Endodermis Elongation_Endodermis
40 5042
Maturation_Endodermis Proliferation Domain_Procambium
2327 5
Transition Domain_Procambium Elongation_Procambium
55 7793
Maturation_Procambium Proliferation Domain_Pericycle
1420 237
Transition Domain_Pericycle Elongation_Pericycle
338 9681
Maturation_Pericycle Proliferation Domain_Phloem
1746 49
Transition Domain_Phloem Elongation_Phloem
378 2393
Maturation_Phloem Proliferation Domain_Xylem
296 107
Transition Domain_Xylem Elongation_Xylem
66 3052
Maturation_Xylem
554
order
## BL2
bl2$time.celltype.anno.Li.crude <- factor(bl2$time.celltype.anno.Li.crude, levels = order[sort(match(unique(bl2$time.celltype.anno.Li.crude),order))])
options(repr.plot.width=14, repr.plot.height=10)
DotPlot(object = bl2, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")+scale_y_discrete(breaks=order, labels=order) + ylab("")
options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = bl2, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("") + theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot
options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black")
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")
dot
ggsave("../BL_2hours_cell_dev_marker_dot_20220808.pdf", width=12, height=10)
## BRZ
brz$time.celltype.anno.Li.crude <- factor(brz$time.celltype.anno.Li.crude, levels = order[sort(match(unique(brz$time.celltype.anno.Li.crude),order))])
options(repr.plot.width=14, repr.plot.height=10)
DotPlot(object = brz, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = brz, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("") + theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot
options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black")
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")
dot
ggsave("../BRZ_cell_dev_marker_dot_20220808.pdf", width=12, height=10)
## BL time course
Idents(rc.integrated) <- "time.celltype.anno.Li.crude"
DefaultAssay(rc.integrated) <- "integrated"
rc.integrated$time.celltype.anno.Li.crude <- factor(rc.integrated$time.celltype.anno.Li.crude, levels = order[sort(match(unique(rc.integrated$time.celltype.anno.Li.crude),order))])
options(repr.plot.width=14, repr.plot.height=10)
DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("") + theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot
options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black")
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")
dot
## WT atlas
Idents(rc.integrated) <- "time.celltype.anno.Li.crude"
DefaultAssay(rc.integrated) <- "integrated"
rc.integrated$time.celltype.anno.Li.crude <- factor(rc.integrated$time.celltype.anno.Li.crude, levels = order[sort(match(unique(rc.integrated$time.celltype.anno.Li.crude),order))])
options(repr.plot.width=14, repr.plot.height=10)
DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() +
scale_x_discrete(breaks=breaks, labels=labels) + xlab("")
options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("") + theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
scale_x_discrete(breaks=breaks, labels=labels) + xlab("")
dot
options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") +
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black")
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") +
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")
dot
ann_df <- tibble(timezone=as.character(Markers_to_plot$timezone),
celltype= as.character(Markers_to_plot$celltype)) %>%
mutate(row=dplyr::row_number(),
col=rep("A")) %>%
group_by(celltype) %>%
mutate(ct_row=dplyr::row_number()) %>%
ungroup() %>%
mutate(Label=celltype)
#ann_df$Label[ann_df$celltype=="Metaphloem & Companion Cell"] <- "Metaphloem & CC"
ann_df$Label[ann_df$ct_row!=3] <- " "
ann_df$Label[ann_df$celltype=="Quiescent Center"] <- "Quiescent Center"
ann_df$Label[(ann_df$celltype=="Columella") & (ann_df$ct_row==2)] <- "Columella"
ann_df$Label[(ann_df$celltype=="Lateral Root Cap") & (ann_df$ct_row==2)] <- "Lateral Root Cap"
ann_df$row <- factor(ann_df$row)
ann_df$timezone <- factor(ann_df$timezone, levels=c("Proliferation Domain", "Transition Domain", "Elongation", "Maturation", "Proximal Lateral Root Cap", "Distal Lateral Root Cap", "Proximal Columella", "Distal Columella"))
options(repr.plot.width=1, repr.plot.height=10)
(time_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, fill=timezone)) + geom_tile() + scale_fill_manual(values = c('#F7E7B0','#FFC400','#2B871F','#005E3B',"#deebf7", "#3182bd", '#fee0d2','#de2d26')) +theme_nothing())
options(repr.plot.width=3, repr.plot.height=10)
ann_df %>% ggplot(aes(x=col, y=row, fill=timezone)) + geom_tile() + scale_fill_manual(values = c('#F7E7B0','#FFC400','#2B871F','#005E3B',"#deebf7", "#3182bd", '#fee0d2','#de2d26')) + theme_minimal()
order <- c("Quiescent Center", "Ground Tissue","Columella", "Lateral Root Cap", "Atrichoblast", "Trichoblast", "Cortex", "Endodermis", "Phloem","Protophloem", "Xylem", "Procambium","Pericycle","Phloem Pole Pericycle", "Protoxylem", "Metaxylem", "Unknown")
palette <- c("#9400d3", "#DCD0FF","#5ab953", "#bfef45", "#008080", "#21B6A8", "#82b6ff", "#0000FF","#e6194b", "#dd77ec", "#9a6324", "#ffe119", "#ff9900", "#ffd4e3", "#9a6324", "#ddaa6f", "#EEEEEE")
options(repr.plot.width=1, repr.plot.height=10)
ann_df$celltype <- factor(ann_df$celltype, levels = order[sort(match(unique(ann_df$celltype),order))])
color <- palette[sort(match(unique(ann_df$celltype),order))]
(cell_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, fill=celltype)) + geom_tile() + scale_fill_manual(values = color) + theme_nothing())
options(repr.plot.width=1, repr.plot.height=10)
cell_ann_p | time_ann_p
options(repr.plot.width=3.5, repr.plot.height=10)
(text_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, label=Label)) + geom_text(size = 4) + theme(plot.margin = margin(0, 0, 35, 35, "cm")) + theme_nothing())
options(repr.plot.width=4, repr.plot.height=10)
(c_ann <- text_ann_p | (cell_ann_p | time_ann_p))
# BL 2 hours
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork
combined_marker_plot
ggsave("../BL_2hours_cell_dev_marker_dot_20220808.pdf", width=15, height=10)
# BRZ
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot
ggsave("../BRZ_cell_dev_marker_dot_20220808.pdf", width=15, height=10)
## BL time course
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot
## WT atlas
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot
ggsave("../Atlas_cell_dev_marker_dot_20220310.pdf", width=15, height=10)
sessionInfo()
R version 3.6.1 (2019-07-05) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Matrix products: default BLAS/LAPACK: /home/tmnolan7/anaconda3/envs/r_3.6.1/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggrepel_0.8.2 gprofiler2_0.1.8 GeneOverlap_1.22.0 [4] circlize_0.4.8 ComplexHeatmap_2.2.0 cowplot_1.0.0 [7] future_1.17.0 RColorBrewer_1.1-2 Seurat_3.1.5 [10] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 [13] purrr_0.3.3 readr_1.3.1 tidyr_1.0.2 [16] tibble_3.0.1 ggplot2_3.3.0 tidyverse_1.3.0 loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_1.4-1 rjson_0.2.20 [4] ellipsis_0.3.0 ggridges_0.5.2 IRdisplay_0.7.0 [7] GlobalOptions_0.1.1 base64enc_0.1-3 fs_1.4.1 [10] clue_0.3-57 rstudioapi_0.11 farver_2.0.3 [13] leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0 [16] fansi_0.4.1 lubridate_1.7.8 xml2_1.3.0 [19] codetools_0.2-16 splines_3.6.1 lsei_1.2-0 [22] IRkernel_1.1 jsonlite_1.6.1 broom_0.5.5 [25] ica_1.0-2 cluster_2.1.0 dbplyr_1.4.2 [28] png_0.1-7 uwot_0.1.8 sctransform_0.2.1 [31] compiler_3.6.1 httr_1.4.1 backports_1.1.7 [34] assertthat_0.2.1 Matrix_1.2-18 lazyeval_0.2.2 [37] cli_2.0.2 htmltools_0.4.0 tools_3.6.1 [40] rsvd_1.0.3 igraph_1.2.5 gtable_0.3.0 [43] glue_1.4.1 RANN_2.6.1 reshape2_1.4.3 [46] rappdirs_0.3.1 Rcpp_1.0.4.6 cellranger_1.1.0 [49] vctrs_0.2.4 gdata_2.18.0 ape_5.3 [52] nlme_3.1-145 lmtest_0.9-37 globals_0.12.5 [55] rvest_0.3.5 lifecycle_0.2.0 irlba_2.3.3 [58] gtools_3.8.2 MASS_7.3-51.5 zoo_1.8-8 [61] scales_1.1.1 hms_0.5.3 parallel_3.6.1 [64] gridExtra_2.3 reticulate_1.15 pbapply_1.4-2 [67] stringi_1.4.3 caTools_1.18.0 shape_1.4.4 [70] repr_1.1.0 rlang_0.4.6 pkgconfig_2.0.3 [73] bitops_1.0-6 evaluate_0.14 lattice_0.20-41 [76] ROCR_1.0-7 labeling_0.3 patchwork_1.0.0.9000 [79] htmlwidgets_1.5.1 tidyselect_1.0.0 RcppAnnoy_0.0.16 [82] plyr_1.8.6 magrittr_1.5 R6_2.4.1 [85] gplots_3.0.3 generics_0.0.2 pbdZMQ_0.3-3 [88] DBI_1.1.0 pillar_1.4.3 haven_2.2.0 [91] withr_2.2.0 fitdistrplus_1.0-14 RCurl_1.98-1.2 [94] survival_3.1-11 tsne_0.1-3 future.apply_1.4.0 [97] modelr_0.1.6 crayon_1.3.4 uuid_0.1-4 [100] KernSmooth_2.23-16 plotly_4.9.2.1 GetoptLong_0.1.8 [103] readxl_1.3.1 data.table_1.12.8 reprex_0.3.0 [106] digest_0.6.25 munsell_0.5.0 viridisLite_0.3.0